Transcript Octave`s presentation on WW domain

Using Sequence Information
Into Protein Docking Procedure
What did we want to do ?
Why did we want to do that ?
How did we want to do that ?
What did we want to do?

Incorporate sequence and experimental
information into protein-protein or proteinligand docking procedure

Test the method by treating the case when
two proteins are known to bind and 3D
modells are available for both binding
partners
Why did we want to do that?
Importance of protein-protein interaction in cellular processes
We therefore need accurate tools to predict such events
Methods exist with attempt to predict protein-protein docking
Base on :
• Shape complementarity (Shoichet & Kuntz, 1996; Janin et al., 1995)
• Surface match (Helmer-Citterich &Tramontano, 1994; Walls & Sternberg, 1992)
• Electrostatic (Gabdoulline & Wade, 1998; Vijayakumar et al., 1998)
• Combination of some of the above strategy (Gabb et al., 1997)
Sequence and structural data are actually on increase
The need for combining sequence and structural information to:
Improve existing methods
Generate new approaches
To predict protein-protein/ligand docking is urgent
How did we want to do that?
Define type of protein sequence to use
Find out conserved residues in that protein family or subfamily
Find out experimental and structural
information available in the literatures
Combine sequence and experimental
Information to select residues to use to define
distance constraints in the sdabf program (gabdoulline and Wade, 2002)
Hope to make sampling more faster comparing to not
using sequence and experimental information
Hope to have correct docked structure and avoid
false positives when sequence and experimental
information are used
WW domain alignment
The WW domain
Definition: The WW domain is a protein-protein interaction module
compose of 35-40 amino acids. It has 3 anti-parallel beta-sheet,
and is stable in the absence of disulfide bonds, cofactor or ligands
P37
W11
W34
F25
Y23
The domain binds proline-rich
or proline containing ligands
it is evolutionary well conserved and
present in plants, yeast, worm,
fly and vertebrates
Classification of WW domains
Groups/representatives
Consensus sequence of the ligand
Representative ligands
PPxY
PEBP2 transcriptional activator,
ENaC sodium channel, beta-dystroglycan
PPPPPPL/RP
Formin, Mena, Bat2
(PxxGMxPP)N
Splicing factors: SmB, SmB', U1C
Phospho-(S/T)P
RNA Pol II, Cdc25C, p53
Rx(x)PPGPPPxR
NpwBP
Group I
YAP65, Nedd4,
Dystrophin
Group II
Formin Binding Proteins,
FE65
Group III
Formin Binding Proteins
Group IV
Ess1/Pin1
Group V
Npw38/PQBP-1
http://www.bork.embl-heidelberg.de/Modules/ww_classes.html
Function of the WW domain
Variety of target
Therefore involve in variety of cellular processes such as:
- Co-activation of transcription and modulation of RNA pol II
- Mitotic regulation (G2/M transition)
- Protein processing …
Implicate in several human diseases such as:
- Muscular Dystrophy
- Alzheimer’s disease
- Hypertension
- Cancer …
Differences between the
free and complexed pin1 WW domain
Sequence alignment,
experimental information
PDB-file 1f8a
Script „pdbExtractor“
file with coordinates of the
WW-domain
file with coordinates of the
phosphorylated peptide
remove phosphates
coordinates of the dephosphorylated peptide
Script„do_all_whatif“:
add the H-atoms with “Whatif”
dephosphorylated peptide +H-atoms
+PO3- ; -HG of SER
p1.pdb
p2.pdb
Script „do_bf_prepare”:
UHBD, ECM,
mk_ds_grid
p1e.grd, p1.echa, p1ds.grd
p1.rxna
p2e.grd, p2.echa, p2ds.grd
p2.rxna
Script
„rxnaEditor.py“
+ other parameters (e.g. the distance constraint)
sdabf12.in (input-file)
Script „do-run“
start the simulation
sdabfcw
fort.xx* and other output-files
Nmrclust, twopdb2rmsd.f, clusteranalyse.f
Clustering and cluster analysis
could sampling be speed up using
sequence/experimental information?
constraints
SDABF
(grid sampling)
0
1
2
3
30.5h
4-6h
6-9h
8-13h
ca 2h
5-8min
1h (W34)?
6min
1-2.5h
sampling time
SDA
(BD sampling)
E12= Ecoul + Edes
E12= Ecoul
E12= Ecoul + Edes + Ehyd
E12= Ecoul + Edes
E12= Ecoul
E12= Ecoul + Edes + Ehyd
ComplexCen
Y27
FreeCen
Y23
RMSD
program
free WW domain
constraint
SDABF
(grid sampling)
SDA
(BD sampling)
complexed WW domain
0
Y23
0
Y27
17.9
19.4
25.7
23.8
10.2
25.7
23.0
9.5
18.1
18.7
5.5
6.4
8.2
7.5
11.5
13.2
9.2
10.5
4.2
8.0
3.6
10.0
9.4
14.2
4.2
6.2
10.3
15.9
15.0
9.7
3.6
14.5
15.4
6.0
11.8
12.6
11.0
13.4
14.5
13.0
18.1
17.8
18.5
24.9
19.0
18.9
18.9
17.3
25.9
26.1
9.7
12.3
7.2
7.1
13.5
9.3
5.0
14.5
12.9
12.1
2.8
2.7
2.4
3.0
3.4
3.7
2.5
3.0
3.1
3.0
2.4
3.0
2.4
2.9
2.9
3.2
2.8
2.8
3.0
2.2
W38
Y27
W34
Y23
RMSD
program
free WW domain
constraint
SDABF
(grid sampling)
SDA
(BD sampling)
complexed WW domain
W34
Y23
W38
Y27
23.8
23.0
25.1
22.1
8.8
13.5
20.9
22.1
22.1
10.6
5.5
6.4
8.2
7.5
11.5
13.2
9.2
10.5
4.2
8.0
3.6
14.2
4.2
10.3
15.9
15.0
9.7
10.3
11.4
15.4
3.6
14.5
15.4
6.0
11.8
12.6
11.0
13.4
14.5
13.0
8.1
24.3
24.8
20.5
10.3
25.8
8.2
18.4
22.9
22.4
9.7
12.3
7.2
7.1
13.5
9.3
5.0
14. 5
12.9
12.1
2.4
3.0
3.0
3.6
2.8
3.4
4.6
3.2
2.8
5.2
2.4
3.0
2.4
2.9
2.9
3.2
2.8
2.8
3.0
2.2
RMSD
Program
free WW domain
Constraint
SDABF
(grid sampling)
complexed WW domain
R17Y23
W34Y23*
R21Y27
W38Y27
7.471
11.078
12.859
10.838
13.795
11.513
12.543
14.428
13.468
12.956
8.794
8.149
10.636
8.606
10.505
8.792
7.386
8.357
11.018
8.497
17.814
10.815
13.899
16.749
17.944
17.677
17.006
13.339
18.032
16.458
3.474
10.340
15.363
14.461
11.369
11.184
6.723
11.958
10.046
12.838
SDA
(BD sampling)
*Independent distance = 6
7.210
6.573
10.384
6.314
9.314
10.434
16.834
8.327
10.045
16.688
R21Y27W38
Grid sampling
R17Y23W34
R21Y27W38
R17Y23W34
BD sampling
program
SDABF
ENERGY
SDA
R17Y23W34
program
R21Y27W38
-6,4284
-6,4263
-6,1933
-6,1869
-6,1372
-6,0129
-5,9385
-5,6976
-5,6498
-5,6457
-13,523
-11,443
-10,171
-9,4154
-8,7401
-8,484
-7,9132
-7,5226
-7,3882
-6,8053
-6,31
-5,98
-5,92
-5,8
-5,78
-5,76
-5,75
-5,74
-5,71
-5,69
-16,3
-16,2
-16,0
-15,9
-15,9
-15,8
-15,8
-15,7
-15,7
-15,7
SDABF
RMSD
SDA
R17Y23W34
R21Y27W38
17,737
17,809
4,221
4,192
4,628
3,072
6,713
15,895
4,935
4,412
4,510
6,674
11,710
15,191
15,835
13,062
13,853
10,941
11,070
11,476
6,214
17,543
4,241
2,430
4,945
3,669
15,556
5,661
4,266
3,063
2,808
2,749
2,362
3,041
2,364
3,401
3,504
3,656
2,455
3,342
Conclusion
RUN TIME
constraint
SDABF
SDA
0
1
2
3
30.5h
4-6h
6h40min
8-13h
ca 2h
5-8min
1h (W34)?
6min
1-2.5h
RMSD
free WW domain
constraint
SDABF
0
W34
Y23
R17Y23
W34Y23
R17Y23W34
17.875
9.452
23.832
8.794
5.491
4.221
7.471
8.794
7.4
17,737
3,072
18.138
17.297
8.117
9.714
5.021
7.210
6.314
6,214
2,430
(grid sampling)
SDA
(BD sampling)
RMSD
docked WW domain
constraint
SDABF
0
W38
Y27
R21Y27
W38Y27
R21Y27W38
3.586
3.586
3.611
17.814
10.815
3.474
4,510
2.808
2.455
2.362
2.362
2.249
(grid sampling)
SDA
(BD sampling)
2,808
2,362
Thanks to
All the MCM -GROUP members
Special thanks to
Rebecca Wade
Razif Gabdoulline
Jan Lac and Ting Wang